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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ), 'gf_id' => 'HOM05D001099', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001099' ), 'data_identifier' => 'HOM05D001099', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001099', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16470' => 'bna', 'A01p19110' => 'bna', 'A03p16190' => 'bna', 'A10p09350' => 'bna', 'Aa31LG7G10380' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5017' => 'aag', 'Actinidia02125' => 'ach', 'Actinidia02128' => 'ach', 'Actinidia08103' => 'ach', 'Actinidia12873' => 'ach', 'Actinidia14437' => 'ach', 'Actinidia28278' => 'ach', 'Actinidia30686' => 'ach', 'Actinidia34260' => 'ach', 'Ah.06g191050' => 'amhyb', 'Ah.06g191060' => 'amhyb', 'Ah.06g191070' => 'amhyb', 'Ah.07g204800' => 'amhyb', 'Ah.07g204810' => 'amhyb', 'Ah.08g211490' => 'amhyb', 'Ah.12g056780' => 'amhyb', 'AL7G24990' => 'aly', 'AL7G27950' => 'aly', 'AL8G25730' => 'aly', 'Aqoxy1G01113' => 'aox', 'Aqoxy3G00413' => 'aox', 'Aqoxy5G01280' => 'aox', 'Aqoxy5G03464' => 'aox', 'Aqoxy5G03580' => 'aox', 'Aqoxy5G03699' => 'aox', 'Aqoxy5G03895' => 'aox', 'Aqoxy5G03896' => 'aox', 'Aqoxy5G03897' => 'aox', 'Aqoxy5G03898' => 'aox', 'Aqoxy5G03899' => 'aox', 'Aqoxy5G03900' => 'aox', 'Aqoxy5G04287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4VI3J6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K80GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IVRK3W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PCT7KU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR3Y2J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQI4QJ' => 'arhy', 'AT4G25200' => 'ath', 'AT4G27670' => 'ath', 'AT5G51440' => 'ath', 'ATR0078G019' => 'atr', 'ATR0824G132' => 'atr', 'Atru.chr1.726' => 'acertr', 'Atru.chr1.727' => 'acertr', 'Atru.chr11.2215' => 'acertr', 'Atru.chr12.2398' => 'acertr', 'Atru.chr6.2475' => 'acertr', 'Atru.chr9.1326' => 'acertr', 'AUR62000518' => 'cqu', 'AUR62000519' => 'cqu', 'AUR62000520' => 'cqu', 'AUR62000521' => 'cqu', 'AUR62000522' => 'cqu', 'AUR62006016' => 'cqu', 'AUR62006861' => 'cqu', 'AUR62006862' => 'cqu', 'AUR62006864' => 'cqu', 'AUR62006865' => 'cqu', 'AUR62006866' => 'cqu', 'AUR62006867' => 'cqu', 'AUR62007509' => 'cqu', 'AUR62014835' => 'cqu', 'AUR62014836' => 'cqu', 'AUR62017031' => 'cqu', 'AUR62026932' => 'cqu', 'AUR62026933' => 'cqu', 'AUR62035610' => 'cqu', 'AUR62039962' => 'cqu', 'AUR62041576' => 'cqu', 'AUR62041577' => 'cqu', 'BcaB08g35500' => 'bca', 'BcaC01g06086' => 'bca', 'BcaC01g06120' => 'bca', 'BcaC04g20675' => 'bca', 'BcaC09g50550' => 'bca', 'BcaC09g50798' => 'bca', 'BcaNung01641' => 'bca', 'BcaNung06351' => 'bca', 'BolC1t01993H' => 'bol', 'BolC1t02359H' => 'bol', 'BolC3t14295H' => 'bol', 'BolC9t56952H' => 'bol', 'BraA01t01601Z' => 'bra', 'BraA01t01853Z' => 'bra', 'BraA03t10910Z' => 'bra', 'BraA10t43011Z' => 'bra', 'C01p20640' => 'bna', 'C01p24030' => 'bna', 'C03p19070' => 'bna', 'C09p40730' => 'bna', 'CAN.G1218.24' => 'can', 'CAN.G1367.2' => 'can', 'CAN.G1367.3' => 'can', 'CAN.G164.15' => 'can', 'CAN.G303.8' => 'can', 'CANSAT01G0592' => 'cansat', 'CANSAT21G0926' => 'cansat', 'CANSAT56G2602' => 'cansat', 'CANSAT56G3256' => 'cansat', 'CARHR232600' => 'chi', 'CARHR235400' => 'chi', 'CARHR264170' => 'chi', 'CARHR292920' => 'chi', 'Carub.0007s1315' => 'cru', 'Carub.0007s1583' => 'cru', 'Carub.0008s1146' => 'cru', 'Ca_14749_v3' => 'car', 'Ca_16495_v3' => 'car', 'Ca_16765_v3' => 'car', 'Ca_19626_v3' => 'car', 'Cc02_g00910' => 'ccan', 'Cc02_g04250' => 'ccan', 'Cc08_g12550' => 'ccan', 'Cc08_g12560' => 'ccan', 'Cc08_g12570' => 'ccan', 'Cc08_g12590' => 'ccan', 'Cc11_g16360' => 'ccan', 'CDE03G0474' => 'cde', 'CDE04G0680' => 'cde', 'CDE05G0669' => 'cde', 'CDE05G1243' => 'cde', 'CDE05G1533' => 'cde', 'CDE06G2649' => 'cde', 'CDE07G1226' => 'cde', 'Cfa009285' => 'cfa', 'Cfa012707' => 'cfa', 'Ciclev10005925m.g' => 'ccl', 'Ciclev10006241m.g' => 'ccl', 'Ciclev10016547m.g' => 'ccl', 'Ciclev10022024m.g' => 'ccl', 'Ciclev10023715m.g' => 'ccl', 'Ciclev10032587m.g' => 'ccl', 'CiPaw.05G174800' => 'cil', 'CiPaw.05G203400' => 'cil', 'CiPaw.12G109200' => 'cil', 'ClCG01G000120' => 'cla', 'ClCG04G005380' => 'cla', 'ClCG05G026230' => 'cla', 'ClCG10G002740' => 'cla', 'COL.COLO4_14123' => 'col', 'COL.COLO4_14358' => 'col', 'COL.COLO4_37189' => 'col', 'Cpa.g.sc29.146' => 'cpa', 'Cpa.g.sc3.147' => 'cpa', 'Cpa.g.sc3.235' => 'cpa', 'Cpa.g.sc3.323' => 'cpa', 'CsaV3_3G002770' => 'csa', 'CsaV3_3G002780' => 'csa', 'CsaV3_5G000040' => 'csa', 'CsaV3_5G030610' => 'csa', 'CSS0007076' => 'camsi', 'CSS0016514' => 'camsi', 'CSS0020189' => 'camsi', 'CSS0020379' => 'camsi', 'CSS0025641' => 'camsi', 'CSS0029931' => 'camsi', 'CSS0030519' => 'camsi', 'CSS0036209' => 'camsi', 'CSS0040337' => 'camsi', 'CSS0044934' => 'camsi', 'CSS0047915' => 'camsi', 'DCAR_008975' => 'dca', 'DCAR_024078' => 'dca', 'DCAR_026487' => 'dca', 'DCAR_027780' => 'dca', 'DCAR_027781' => 'dca', 'Dinv14779' => 'din', 'Dinv21628' => 'din', 'Dinv21629' => 'din', 'Dinv21630' => 'din', 'Dinv21631' => 'din', 'Dinv21632' => 'din', 'Dinv24640' => 'din', 'Dinv28574' => 'din', 'Dinv29220' => 'din', 'Dinv39132' => 'din', 'Dinv39133' => 'din', 'Dinv39134' => 'din', 'Dinv39136' => 'din', 'Dinv39137' => 'din', 'Dinv39138' => 'din', 'Duzib068G0845' => 'dzi', 'Duzib205G0330' => 'dzi', 'Duzib205G1413' => 'dzi', 'Duzib248G0292' => 'dzi', 'Duzib268G1734' => 'dzi', 'ECA233G2893' => 'eca', 'ECA233G4167' => 'eca', 'ECA233G5101' => 'eca', 'ECA240G1483' => 'eca', 'EL10Ac3g05195' => 'bvu', 'EL10Ac4g09625' => 'bvu', 'EL10Ac4g09626' => 'bvu', 'EL10Ac4g09627' => 'bvu', 'EL10Ac4g09628' => 'bvu', 'EL10Ac4g09629' => 'bvu', 'EL10Ac5g13076' => 'bvu', 'EL10Ac7g16670' => 'bvu', 'EL10Ac8g19121' => 'bvu', 'EL10Ac8g20401' => 'bvu', 'EL10Ac9g21028' => 'bvu', 'Eucgr.A01416' => 'egr', 'Eucgr.D02070' => 'egr', 'Eucgr.D02073' => 'egr', 'Eucgr.E00433' => 'egr', 'Eucgr.H04692' => 'egr', 'Eucgr.K00423' => 'egr', 'Eucgr.L02980' => 'egr', 'FAN01G0396' => 'fan', 'FAN01G0971' => 'fan', 'FAN01G1499' => 'fan', 'FAN01G1585' => 'fan', 'FAN02G3786' => 'fan', 'FAN03G0031' => 'fan', 'FAN03G0428' => 'fan', 'FAN03G0595' => 'fan', 'FAN03G0774' => 'fan', 'FAN03G0999' => 'fan', 'FAN03G1450' => 'fan', 'FAN04G1733' => 'fan', 'FAN04G3139' => 'fan', 'FAN05G3142' => 'fan', 'FAN06G0318' => 'fan', 'FAN06G1895' => 'fan', 'FAN06G3855' => 'fan', 'FAN07G1920' => 'fan', 'FAN08G1760' => 'fan', 'FAN08G1842' => 'fan', 'FAN08G3558' => 'fan', 'FAN09G3490' => 'fan', 'FAN09G3745' => 'fan', 'FAN10G0723' => 'fan', 'FAN10G0801' => 'fan', 'FAN10G1801' => 'fan', 'FAN10G2335' => 'fan', 'FAN10G3023' => 'fan', 'FAN10G3756' => 'fan', 'FAN12G2577' => 'fan', 'FAN13G2298' => 'fan', 'FAN14G3395' => 'fan', 'FAN14G3625' => 'fan', 'FAN14G4560' => 'fan', 'FAN14G4561' => 'fan', 'FAN14G4853' => 'fan', 'FAN17G1345' => 'fan', 'FAN18G3089' => 'fan', 'FAN22G1154' => 'fan', 'FvH4_2g05762' => 'fve', 'FvH4_4g24850' => 'fve', 'FvH4_5g18720' => 'fve', 'FvH4_5g23240' => 'fve', 'FvH4_6g02120' => 'fve', 'FvH4_6g02150' => 'fve', 'FvH4_7g19240' => 'fve', 'FvH4_7g27540' => 'fve', 'FvH4_7g32800' => 'fve', 'Glyma.04G229800' => 'gma', 'Glyma.06G134900' => 'gma', 'Glyma.08G318900' => 'gma', 'Glyma.09G223800' => 'gma', 'Glyma.11G246600' => 'gma', 'Glyma.12G013100' => 'gma', 'Glyma.18G010500' => 'gma', 'Glyma.18G094600' => 'gma', 'Gohir.A04G137700' => 'ghi', 'Gohir.A08G104100' => 'ghi', 'Gohir.A08G170900' => 'ghi', 'Gohir.A12G198400' => 'ghi', 'Gohir.A12G246750' => 'ghi', 'Gohir.D04G180900' => 'ghi', 'Gohir.D08G115600' => 'ghi', 'Gohir.D08G189200' => 'ghi', 'Gohir.D12G201000' => 'ghi', 'Gohir.D12G247450' => 'ghi', 'Gorai.004G124600' => 'gra', 'Gorai.004G199300' => 'gra', 'Gorai.008G216100' => 'gra', 'Gorai.008G265500' => 'gra', 'Gorai.012G174100' => 'gra', 'GSVIVG01001315001' => 'vvi', 'GSVIVG01001316001' => 'vvi', 'GSVIVG01010308001' => 'vvi', 'GSVIVG01018654001' => 'vvi', 'GSVIVG01038631001' => 'vvi', 'HanXRQChr03g0088611' => 'han', 'HanXRQChr08g0207301' => 'han', 'HanXRQChr08g0225741' => 'han', 'HanXRQChr12g0372131' => 'han', 'HanXRQChr13g0418041' => 'han', 'HanXRQChr16g0502971' => 'han', 'Haze_07927' => 'cav', 'Hma1.2p1_0079F.1_g041510' => 'hma', 'Hma1.2p1_0094F.1_g047280' => 'hma', 'Hma1.2p1_0415F.1_g148120' => 'hma', 'Hma1.2p1_0415F.1_g148130' => 'hma', 'Hma1.2p1_0432F.1_g151730' => 'hma', 'Hma1.2p1_1132F.1_g260310' => 'hma', 'Hma1.2p1_1132F.1_g260320' => 'hma', 'Hma1.2p1_1172F.1_g263520' => 'hma', 'Hma1.2p1_1172F.1_g263530' => 'hma', 'Hma1.2p1_1640F.1_g295060' => 'hma', 'Hma1.2p1_1640F.1_g295063' => 'hma', 'Hma1.2p1_1704F.1_g298350' => 'hma', 'Hma1.2p1_1786F.1_g302310' => 'hma', 'Hma1.2p1_1786F.1_g302330' => 'hma', 'Hma1.2p1_1786F.1_g302340' => 'hma', 'HPP92_005991' => 'vpl', 'HPP92_007342' => 'vpl', 'HPP92_011662' => 'vpl', 'HPP92_011701' => 'vpl', 'HPP92_013099' => 'vpl', 'HPP92_013109' => 'vpl', 'HPP92_013547' => 'vpl', 'HPP92_022253' => 'vpl', 'Hund06055' => 'sun', 'Hund09705' => 'sun', 'Hund11593' => 'sun', 'Hund14531' => 'sun', 'Hund21047' => 'sun', 'Hund21048' => 'sun', 'Hund21049' => 'sun', 'Hund21051' => 'sun', 'Lalb_Chr01g0000691' => 'lal', 'Lalb_Chr08g0230771' => 'lal', 'Lalb_Chr08g0239771' => 'lal', 'Lj1A1027T36' => 'lonja', 'Lj1g0004957' => 'lja', 'Lj2P216T41' => 'lonja', 'Lj3g0025824' => 'lja', 'Lj6g0024762' => 'lja', 'Lj6g0025217' => 'lja', 'Lj8P261T44' => 'lonja', 'Lj8P261T47' => 'lonja', 'Lsat_1_v5_gn_3_481' => 'lsa', 'Lsat_1_v5_gn_6_91340' => 'lsa', 'Lsat_1_v5_gn_8_151001' => 'lsa', 'Lsat_1_v5_gn_8_4541' => 'lsa', 'Manes.01G042200' => 'mes', 'Manes.06G134700' => 'mes', 'Manes.12G017300' => 'mes', 'Manes.13G013400' => 'mes', 'Manes.14G036000' => 'mes', 'Mapoly0091s0087' => 'mpo', 'MBI05_g10091_MAGBIO' => 'mbi', 'MBI05_g11985_MAGBIO' => 'mbi', 'MBI12_g16190_MAGBIO' => 'mbi', 'MD01G1227600' => 'mdo', 'MD06G1060300' => 'mdo', 'MD07G1253800' => 'mdo', 'MD07G1298000' => 'mdo', 'MD13G1108500' => 'mdo', 'MD13G1120200' => 'mdo', 'MD16G1108600' => 'mdo', 'Medtr0004s0510' => 'mtr', 'Medtr0036s0250' => 'mtr', 'Medtr0361s0010' => 'mtr', 'Medtr3g052760' => 'mtr', 'Medtr3g086050' => 'mtr', 'Medtr3g092460' => 'mtr', 'Medtr4g088455' => 'mtr', 'Medtr7g102590' => 'mtr', 'MELO3C005923.2' => 'cme', 'MELO3C011908.2' => 'cme', 'MELO3C013945.2' => 'cme', 'MELO3C013946.2' => 'cme', 'Migut.C00061' => 'egut', 'Migut.C00062' => 'egut', 'Migut.C00064' => 'egut', 'Migut.C00065' => 'egut', 'Migut.E00230' => 'egut', 'Migut.F00477' => 'egut', 'Migut.F00478' => 'egut', 'Migut.F01183' => 'egut', 'Migut.H01086' => 'egut', 'MSTRG.129' => 'ama', 'MSTRG.26985' => 'ama', 'MSTRG.27200' => 'ama', 'MSTRG.27202' => 'ama', 'MSTRG.8412' => 'ama', 'MSTRG.8615' => 'ama', 'Nitab4.5_0000041g0340' => 'nta', 'Nitab4.5_0000312g0130' => 'nta', 'Nitab4.5_0000312g0140' => 'nta', 'Nitab4.5_0000319g0220' => 'nta', 'Nitab4.5_0001318g0050' => 'nta', 'Nitab4.5_0006389g0020' => 'nta', 'Nitab4.5_0007598g0030' => 'nta', 'Nn1g01033' => 'nnu', 'Nn1g06538' => 'nnu', 'Nn1g06637' => 'nnu', 'Nn3g16578' => 'nnu', 'Nn4g25829' => 'nnu', 'Nn4g26381' => 'nnu', 'Nn6g33979' => 'nnu', 'Oeu019999.1' => 'oeu', 'Oeu020323.1' => 'oeu', 'Oeu021657.1' => 'oeu', 'Oeu022488.1' => 'oeu', 'Oeu023682.1' => 'oeu', 'Oeu035950.1' => 'oeu', 'Oeu038321.1' => 'oeu', 'Os02g0201000' => 'osa', 'Os02g0758000' => 'osa', 'Os03g0245800' => 'osa', 'Os03g0835700' => 'osa', 'Os06g0219500' => 'osa', 'Peaxi162Scf00002g00191' => 'pax', 'Peaxi162Scf00023g01123' => 'pax', 'Peaxi162Scf00128g00741' => 'pax', 'Peaxi162Scf00300g00829' => 'pax', 'Peaxi162Scf00797g00012' => 'pax', 'PGR031G0040' => 'pgr', 'PGR042G1017' => 'pgr', 'PGR042G2034' => 'pgr', 'PGR119G0832' => 'pgr', 'PGR142G4429' => 'pgr', 'PGSC0003DMG400003219' => 'stu', 'PGSC0003DMG400004807' => 'stu', 'PGSC0003DMG400004808' => 'stu', 'PGSC0003DMG400011977' => 'stu', 'Phvul.001G258200' => 'pvu', 'Phvul.006G046000' => 'pvu', 'Phvul.009G046500' => 'pvu', 'Phvul.011G016100' => 'pvu', 'Phvul.011G016200' => 'pvu', 'Potri.003G075900' => 'ptr', 'Potri.003G076000' => 'ptr', 'Potri.003G109200' => 'ptr', 'Potri.006G034600' => 'ptr', 'Potri.009G021400' => 'ptr', 'Potri.010G053400' => 'ptr', 'Potri.012G022400' => 'ptr', 'Potri.015G005801' => 'ptr', 'Pp3c1_7030' => 'ppa', 'Pp3c7_25570' => 'ppa', 'PRCOL_00005183' => 'pco', 'Prupe.1G237800' => 'ppe', 'Prupe.2G317700' => 'ppe', 'Prupe.5G071200' => 'ppe', 'Psat4g136720' => 'psa', 'Psat5g073120' => 'psa', 'Psat5g073280' => 'psa', 'Psat5g093880' => 'psa', 'Psat5g174760' => 'psa', 'Psat5g174800' => 'psa', 'PSO063G5704' => 'pso', 'PSO782G0749' => 'pso', 'PSO782G1367' => 'pso', 'PSO782G2285' => 'pso', 'QL09p007324' => 'qlo', 'QL12p012417' => 'qlo', 'QL12p012439' => 'qlo', 'RcHm_v2.0_Chr1g0374411' => 'rch', 'RcHm_v2.0_Chr1g0382761' => 'rch', 'RcHm_v2.0_Chr4g0431921' => 'rch', 'RcHm_v2.0_Chr7g0203041' => 'rch', 'Rhsim03G0167300' => 'rsi', 'Rhsim03G0167600' => 'rsi', 'Rhsim03G0167700' => 'rsi', 'Rhsim03G0167800' => 'rsi', 'Rhsim03G0168200' => 'rsi', 'Rhsim03G0214500' => 'rsi', 'Rhsim07G0020900' => 'rsi', 'Rhsim09G0209200' => 'rsi', 'Rhsim12G0036900' => 'rsi', 'Sabra01G0133100' => 'sbr', 'Sabra03G0075700' => 'sbr', 'Sabra05G0140300' => 'sbr', 'Sabra06G0023100' => 'sbr', 'Sabra10G0017200' => 'sbr', 'Sabra12G0011400' => 'sbr', 'SalBow2G2546' => 'sbo', 'SalBow6G6877' => 'sbo', 'SalBow8G3255' => 'sbo', 'Sc01g0008520' => 'sci', 'Sc03g0006910' => 'sci', 'Sc03g0006990' => 'sci', 'Sc13g0010200' => 'sci', 'Sed0005232' => 'sed', 'Sed0013728' => 'sed', 'Sed0018283' => 'sed', 'Sed0022054' => 'sed', 'SEGI_13652' => 'sgi', 'SEGI_20528' => 'sgi', 'SEGI_24420' => 'sgi', 'SEGI_33519' => 'sgi', 'SGA_v2.0_scaffold136G34998' => 'sas', 'SGA_v2.0_scaffold238G43953' => 'sas', 'SGA_v2.0_scaffold2G01177' => 'sas', 'SGA_v2.0_scaffold2G01178' => 'sas', 'SGA_v2.0_scaffold2G01204' => 'sas', 'SGA_v2.0_scaffold2G01206' => 'sas', 'SGA_v2.0_scaffold44G16843' => 'sas', 'SGA_v2.0_scaffold4G02380' => 'sas', 'SGA_v2.0_scaffold87G27117' => 'sas', 'SHI13915' => 'shi', 'SMO358G0201' => 'smo', 'SMO358G0394' => 'smo', 'Solyc03g082420.3' => 'sly', 'Solyc05g014280.4' => 'sly', 'Solyc08g078700.2' => 'sly', 'Solyc08g078710.3' => 'sly', 'Sopen03g022140' => 'spe', 'Sopen05g009370' => 'spe', 'Sopen08g027180' => 'spe', 'Sopen08g027190' => 'spe', 'Sp6g13600' => 'spa', 'Sp7g23220' => 'spa', 'Sp7g25650' => 'spa', 'TAR082G0002' => 'tar', 'TAR374G1322' => 'tar', 'TAR375G0093' => 'tar', 'TAR375G0450' => 'tar', 'TAR622G1135' => 'tar', 'THA.LOC104808280' => 'tha', 'THA.LOC104811889' => 'tha', 'Thecc.02G082300' => 'tca', 'Thecc.02G270300' => 'tca', 'Thecc.03G155700' => 'tca', 'Thecc.03G207300' => 'tca', 'Thecc.03G252700' => 'tca', 'Thecc.03G252800' => 'tca', 'Thhalv10014661m.g' => 'esa', 'Thhalv10026184m.g' => 'esa', 'Thhalv10026232m.g' => 'esa', 'TPR.G20264' => 'tpr', 'TPR.G28973' => 'tpr', 'TPR.G33393' => 'tpr', 'TPR.G33778' => 'tpr', 'TWI23G0452' => 'twi', 'TWI36G0065' => 'twi', 'TWI39G0534' => 'twi', 'TWI39G1145' => 'twi', 'TWI75G1299' => 'twi', 'TWI81G0609' => 'twi', 'unitig_736.g22948' => 'ugi', 'vmacro01096' => 'vma', 'vmacro06431' => 'vma', 'vmacro06798' => 'vma', 'vmacro06802' => 'vma', 'vmacro09908' => 'vma', 'vmacro13336' => 'vma', 'VMungo1127G1536' => 'vmu', 'VMungo1309G2540' => 'vmu', 'VMungo1383G2261' => 'vmu', 'Zm00001eb010530' => 'zma', 'Zm00001eb034050' => 'zma', 'Zm00001eb193940' => 'zma', 'Zm00001eb235800' => 'zma', 'Zm00001eb372830' => 'zma' ) $gf_id = 'HOM05D001099' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001099' ) $data_identifier = 'HOM05D001099' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 7, 'aly' => (int) 3, 'aox' => (int) 13, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 22, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 5, 'din' => (int) 15, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 11, 'egr' => (int) 7, 'fan' => (int) 39, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 1, 'hma' => (int) 15, 'vpl' => (int) 8, 'sun' => (int) 8, 'lal' => (int) 3, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 9, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 9, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 6, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372830' $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